Related papers: Lightweight Data Indexing and Compression in Exter…
The Burrows-Wheeler transform (BWT) is a permutation whose applications are prevalent in data compression and text indexing. The bijective BWT (BBWT) is a bijective variant of it. Although it is known that the BWT can be constructed in…
The paper introduces a new lossless, highly robust compression algorithm that similar with LZW algorithm, yet the algorithm discards dictionary processing and uses irregular sequences with massive, random information instead. Then the paper…
Inverted indexes allow to query large databases without needing to search in the database at each query. An important line of research is to construct the most efficient inverted indexes, both in terms of compression ratio and time…
One of the most well-known variants of the Burrows-Wheeler transform (BWT) [Burrows and Wheeler, 1994] is the bijective BWT (BBWT) [Gil and Scott, arXiv 2012], which applies the extended BWT (EBWT) [Mantaci et al., TCS 2007] to the multiset…
We propose a novel approach to reduce memory consumption of the backpropagation through time (BPTT) algorithm when training recurrent neural networks (RNNs). Our approach uses dynamic programming to balance a trade-off between caching of…
The Burrows-Wheeler transform (BWT) is a reversible transform that converts a string $w$ into another string $\mathsf{BWT}(w)$. The size of the run-length encoded BWT (RLBWT) can be interpreted as a measure of repetitiveness in the class of…
We present an algorithm for building the extended BWT (eBWT) of a string collection from its grammar-compressed representation. Our technique exploits the string repetitions captured by the grammar to boost the computation of the eBWT.…
Motivation: Burrows-Wheeler Transform (BWT) is a common component in full-text indices. Initially developed for data compression, it is particularly powerful for encoding redundant sequences such as pangenome data. However, BWT construction…
The suffix array is an efficient data structure for in-memory pattern search. Suffix arrays can also be used for external-memory pattern search, via two-level structures that use an internal index to identify the correct block of suffix…
Binary codes are widely used to represent the data due to their small storage and efficient computation. However, there exists an ambiguity problem that lots of binary codes share the same Hamming distance to a query. To alleviate the…
The Burrows-Wheeler Transform (BWT) is often taught in undergraduate courses on algorithmic bioinformatics, because it underlies the FM-index and thus important tools such as Bowtie and BWA. Its admirers consider the BWT a thing of beauty…
Burrows-Wheeler transform (BWT) is an invertible text transformation that, given a text $T$ of length $n$, permutes its symbols according to the lexicographic order of suffixes of $T$. BWT is one of the most heavily studied algorithms in…
Compared to classical deep neural networks its binarized versions can be useful for applications on resource-limited devices due to their reduction in memory consumption and computational demands. In this work we study deep neural networks…
Indexing highly repetitive strings (i.e., strings with many repetitions) for fast queries has become a central research topic in string processing, because it has a wide variety of applications in bioinformatics and natural language…
The Burrows-Wheeler-Transform (BWT), a reversible string transformation, is one of the fundamental components of many current data structures in string processing. It is central in data compression, as well as in efficient query algorithms…
For text retrieval systems, the assumption that all data structures reside in main memory is increasingly common. In this context, we present a novel incremental inverted indexing algorithm for web-scale collections that directly constructs…
The Burrows-Wheeler Transform is a string transformation that plays a fundamental role for the design of self-indexing compressed data structures. Over the years, researchers have successfully extended this transformation outside the…
Run-length encoding Burrows-Wheeler Transformed strings, resulting in Run-Length BWT (RLBWT), is a powerful tool for processing highly repetitive strings. We propose a new algorithm for online RLBWT working in run-compressed space, which…
This paper presents bsort, a non-comparison-based sorting algorithm for signed and unsigned integers, and floating-point values. The algorithm unifies these cases through an approach derived from binary quicksort, achieving $O(wn)$ runtime…
In 1994, Burrows and Wheeler developed a data compression algorithm which performs significantly better than Lempel-Ziv based algorithms. Since then, a lot of work has been done in order to improve their algorithm, which is based on a…